CMD: salmon quant -i /media/sam/4TB_toshiba/porites/20180419_trinity/Trinity.fasta.salmon_quasi.idx -l ISR -1 /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P01-AGTTCC-READ1-Sequences.txt.gz_val_1.fq.gz -2 /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P01-AGTTCC-READ2-Sequences.txt.gz_val_2.fq.gz -o male_bleached_K5_01  -p 23
### salmon (mapping-based) v0.12.0
### [ program ] => salmon 
### [ command ] => quant 
### [ index ] => { /media/sam/4TB_toshiba/porites/20180419_trinity/Trinity.fasta.salmon_quasi.idx }
### [ libType ] => { ISR }
### [ mates1 ] => { /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P01-AGTTCC-READ1-Sequences.txt.gz_val_1.fq.gz }
### [ mates2 ] => { /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P01-AGTTCC-READ2-Sequences.txt.gz_val_2.fq.gz }
### [ output ] => { male_bleached_K5_01 }
### [ threads ] => { 23 }
Logs will be written to male_bleached_K5_01/logs
[2019-06-10 14:37:06.724] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2019-06-10 14:37:06.724] [jointLog] [warning] 

NOTE: It appears you are running salmon without the `--validateMappings` option.
Mapping validation can generally improve both the sensitivity and specificity of mapping,
with only a moderate increase in use of computational resources. 
Unless there is a specific reason to do this (e.g. testing on clean simulated data),
`--validateMappings` is generally recommended.

[2019-06-10 14:37:06.724] [jointLog] [info] parsing read library format
[2019-06-10 14:37:06.724] [jointLog] [info] There is 1 library.
[2019-06-10 14:37:06.784] [jointLog] [info] Loading Quasi index
[2019-06-10 14:37:06.784] [jointLog] [info] Loading 32-bit quasi index
[2019-06-10 14:37:06.784] [stderrLog] [info] Loading Suffix Array 
[2019-06-10 14:37:08.114] [stderrLog] [info] Loading Transcript Info 
[2019-06-10 14:37:08.556] [stderrLog] [info] Loading Rank-Select Bit Array
[2019-06-10 14:37:08.669] [stderrLog] [info] There were 861,197 set bits in the bit array
[2019-06-10 14:37:08.741] [stderrLog] [info] Computing transcript lengths
[2019-06-10 14:37:08.742] [stderrLog] [info] Waiting to finish loading hash
[2019-06-10 14:37:23.395] [stderrLog] [info] Done loading index
[2019-06-10 14:37:23.395] [jointLog] [info] done
[2019-06-10 14:37:23.395] [jointLog] [info] Index contained 861,197 targets






processed 500,000 fragments
hits: 941,514, hits per frag:  2.15014

processed 1,000,000 fragments
hits: 1,880,242, hits per frag:  2.01143

processed 1,500,000 fragments
hits: 2,820,764, hits per frag:  2.0476

processed 2,000,000 fragments
hits: 3,764,057, hits per frag:  1.90216

processed 2,500,000 fragments
hits: 4,707,898, hits per frag:  1.96021

processed 3,000,001 fragments
hits: 5,646,519, hits per frag:  1.94873

processed 3,500,000 fragments
hits: 6,582,915, hits per frag:  1.92075

processed 4,000,001 fragments
hits: 7,518,931, hits per frag:  1.90741

processed 4,500,000 fragments
hits: 8,456,281, hits per frag:  1.93622

processed 5,000,000 fragments
hits: 9,392,494, hits per frag:  1.90095

processed 5,500,000 fragments
hits: 10,329,360, hits per frag:  1.89895

processed 6,000,000 fragments
hits: 11,266,169, hits per frag:  1.90305

processed 6,500,000 fragments
hits: 12,207,760, hits per frag:  1.89143

processed 7,000,000 fragments
hits: 13,151,747, hits per frag:  1.88702

processed 7,500,000 fragments
hits: 14,100,272, hits per frag:  1.89312

processed 8,000,000 fragments
hits: 15,048,022, hits per frag:  1.88873

processed 8,500,000 fragments
hits: 16,000,572, hits per frag:  1.93068

processed 9,000,000 fragments
hits: 16,951,863, hits per frag:  1.88922

processed 9,500,000 fragments
hits: 17,899,700, hits per frag:  1.89522

processed 10,000,001 fragments
hits: 18,845,412, hits per frag:  1.95854

processed 10,500,000 fragments
hits: 19,791,632, hits per frag:  1.90161

processed 11,000,000 fragments
hits: 20,732,512, hits per frag:  1.90323

processed 11,500,000 fragments
hits: 21,677,099, hits per frag:  1.89011

processed 12,000,001 fragments
hits: 22,618,483, hits per frag:  1.89566

processed 12,500,001 fragments
hits: 23,553,524, hits per frag:  1.92463

processed 13,000,001 fragments
hits: 24,489,673, hits per frag:  1.89214

processed 13,500,001 fragments
hits: 25,428,039, hits per frag:  1.92118

processed 14,000,000 fragments
hits: 26,366,069, hits per frag:  1.91038

processed 14,500,000 fragments
hits: 27,307,468, hits per frag:  1.9331

processed 15,000,001 fragments
hits: 28,250,159, hits per frag:  1.89544

processed 15,500,000 fragments
hits: 29,186,163, hits per frag:  1.89266

processed 16,000,000 fragments
hits: 30,115,557, hits per frag:  1.88819

processed 16,500,000 fragments
hits: 31,049,934, hits per frag:  1.91072

processed 17,000,000 fragments
hits: 31,984,300, hits per frag:  1.88497

processed 17,500,000 fragments
hits: 32,921,796, hits per frag:  1.88714

processed 18,000,000 fragments
hits: 33,857,505, hits per frag:  1.90788

processed 18,500,000 fragments
hits: 34,789,208, hits per frag:  1.88762

processed 19,000,000 fragments
hits: 35,728,504, hits per frag:  1.90437

processed 19,500,001 fragments
hits: 36,683,107, hits per frag:  1.89997

processed 20,000,001 fragments
hits: 37,638,543, hits per frag:  1.88383

processed 21,000,000 fragments
hits: 39,562,397, hits per frag:  1.88622

processed 21,500,001 fragments
hits: 40,512,910, hits per frag:  1.88618

processed 22,000,000 fragments
hits: 41,467,654, hits per frag:  1.89686

processed 22,500,000 fragments
hits: 42,411,944, hits per frag:  1.88874

processed 23,000,000 fragments
hits: 43,368,179, hits per frag:  1.8897

processed 23,500,001 fragments
hits: 44,319,146, hits per frag:  1.89049

processed 24,000,002 fragments
hits: 45,262,339, hits per frag:  1.88901

processed 24,500,000 fragments
hits: 46,208,401, hits per frag:  1.89159[2019-06-10 14:38:29.481] [jointLog] [info] Thread saw mini-batch with a maximum of 8.80% zero probability fragments
[2019-06-10 14:38:29.481] [jointLog] [info] Thread saw mini-batch with a maximum of 8.60% zero probability fragments
[2019-06-10 14:38:29.481] [jointLog] [info] Thread saw mini-batch with a maximum of 8.84% zero probability fragments
[2019-06-10 14:38:29.481] [jointLog] [info] Thread saw mini-batch with a maximum of 9.02% zero probability fragments
[2019-06-10 14:38:29.481] [jointLog] [info] Thread saw mini-batch with a maximum of 8.72% zero probability fragments
[2019-06-10 14:38:29.481] [jointLog] [info] Thread saw mini-batch with a maximum of 8.82% zero probability fragments
[2019-06-10 14:38:29.481] [jointLog] [info] Thread saw mini-batch with a maximum of 8.68% zero probability fragments
[2019-06-10 14:38:29.481] [jointLog] [info] Thread saw mini-batch with a maximum of 8.98% zero probability fragments
[2019-06-10 14:38:29.481] [jointLog] [info] Thread saw mini-batch with a maximum of 8.92% zero probability fragments
[2019-06-10 14:38:29.481] [jointLog] [info] Thread saw mini-batch with a maximum of 8.94% zero probability fragments
[2019-06-10 14:38:29.482] [jointLog] [info] Thread saw mini-batch with a maximum of 9.02% zero probability fragments
[2019-06-10 14:38:29.483] [jointLog] [info] Thread saw mini-batch with a maximum of 8.80% zero probability fragments
[2019-06-10 14:38:29.503] [jointLog] [info] Thread saw mini-batch with a maximum of 9.14% zero probability fragments
[2019-06-10 14:38:29.519] [jointLog] [info] Thread saw mini-batch with a maximum of 8.76% zero probability fragments
[2019-06-10 14:38:29.531] [jointLog] [info] Thread saw mini-batch with a maximum of 8.58% zero probability fragments
[2019-06-10 14:38:29.535] [jointLog] [info] Thread saw mini-batch with a maximum of 8.82% zero probability fragments
[2019-06-10 14:38:29.546] [jointLog] [info] Thread saw mini-batch with a maximum of 9.12% zero probability fragments
[2019-06-10 14:38:29.547] [jointLog] [info] Thread saw mini-batch with a maximum of 8.72% zero probability fragments
[2019-06-10 14:38:29.553] [jointLog] [info] Thread saw mini-batch with a maximum of 8.86% zero probability fragments
[2019-06-10 14:38:29.566] [jointLog] [info] Thread saw mini-batch with a maximum of 8.88% zero probability fragments
[2019-06-10 14:38:29.572] [jointLog] [info] Thread saw mini-batch with a maximum of 9.02% zero probability fragments
[2019-06-10 14:38:29.577] [jointLog] [info] Thread saw mini-batch with a maximum of 9.20% zero probability fragments
[2019-06-10 14:38:29.599] [jointLog] [info] Thread saw mini-batch with a maximum of 8.92% zero probability fragments










[2019-06-10 14:38:30.022] [jointLog] [info] Computed 454,965 rich equivalence classes for further processing
[2019-06-10 14:38:30.022] [jointLog] [info] Counted 17,320,109 total reads in the equivalence classes 
[2019-06-10 14:38:30.047] [jointLog] [warning] 0.00989258% of fragments were shorter than the k used to build the index (31).
If this fraction is too large, consider re-building the index with a smaller k.
The minimum read size found was 20.


[2019-06-10 14:38:30.047] [jointLog] [info] Mapping rate = 69.7073%

[2019-06-10 14:38:30.047] [jointLog] [info] finished quantifyLibrary()
[2019-06-10 14:38:30.048] [jointLog] [info] Starting optimizer
[2019-06-10 14:38:30.471] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2019-06-10 14:38:30.504] [jointLog] [info] iteration = 0 | max rel diff. = 892.823
[2019-06-10 14:38:32.908] [jointLog] [info] iteration = 100 | max rel diff. = 11.1636
[2019-06-10 14:38:35.226] [jointLog] [info] iteration = 200 | max rel diff. = 5.7873
[2019-06-10 14:38:37.632] [jointLog] [info] iteration = 300 | max rel diff. = 2.17947
[2019-06-10 14:38:40.094] [jointLog] [info] iteration = 400 | max rel diff. = 8.69826
[2019-06-10 14:38:42.444] [jointLog] [info] iteration = 500 | max rel diff. = 1.71332
[2019-06-10 14:38:44.803] [jointLog] [info] iteration = 600 | max rel diff. = 0.943092
[2019-06-10 14:38:47.180] [jointLog] [info] iteration = 700 | max rel diff. = 0.830012
[2019-06-10 14:38:49.646] [jointLog] [info] iteration = 800 | max rel diff. = 0.285327
[2019-06-10 14:38:52.036] [jointLog] [info] iteration = 900 | max rel diff. = 0.0959774
[2019-06-10 14:38:54.406] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.381643
[2019-06-10 14:38:56.705] [jointLog] [info] iteration = 1,100 | max rel diff. = 0.230418
[2019-06-10 14:38:59.081] [jointLog] [info] iteration = 1,200 | max rel diff. = 0.204185
[2019-06-10 14:38:59.214] [jointLog] [info] iteration = 1,207 | max rel diff. = 0.009259
[2019-06-10 14:38:59.266] [jointLog] [info] Finished optimizer
[2019-06-10 14:38:59.266] [jointLog] [info] writing output 

CMD: /home/shared/Trinityrnaseq-v2.8.5/util/support_scripts/salmon_trans_to_gene_results.pl male_bleached_K5_01/quant.sf /media/sam/4TB_toshiba/porites/20180419_trinity/Trinity.fasta.gene_trans_map > male_bleached_K5_01/quant.sf.genes
CMD: salmon quant -i /media/sam/4TB_toshiba/porites/20180419_trinity/Trinity.fasta.salmon_quasi.idx -l ISR -1 /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P06-GCCAAT-READ1-Sequences.txt.gz_val_1.fq.gz -2 /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P06-GCCAAT-READ2-Sequences.txt.gz_val_2.fq.gz -o male_bleached_K5_02  -p 23
### salmon (mapping-based) v0.12.0
### [ program ] => salmon 
### [ command ] => quant 
### [ index ] => { /media/sam/4TB_toshiba/porites/20180419_trinity/Trinity.fasta.salmon_quasi.idx }
### [ libType ] => { ISR }
### [ mates1 ] => { /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P06-GCCAAT-READ1-Sequences.txt.gz_val_1.fq.gz }
### [ mates2 ] => { /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P06-GCCAAT-READ2-Sequences.txt.gz_val_2.fq.gz }
### [ output ] => { male_bleached_K5_02 }
### [ threads ] => { 23 }
Logs will be written to male_bleached_K5_02/logs
[2019-06-10 14:39:16.480] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2019-06-10 14:39:16.480] [jointLog] [warning] 

NOTE: It appears you are running salmon without the `--validateMappings` option.
Mapping validation can generally improve both the sensitivity and specificity of mapping,
with only a moderate increase in use of computational resources. 
Unless there is a specific reason to do this (e.g. testing on clean simulated data),
`--validateMappings` is generally recommended.

[2019-06-10 14:39:16.480] [jointLog] [info] parsing read library format
[2019-06-10 14:39:16.480] [jointLog] [info] There is 1 library.
[2019-06-10 14:39:16.539] [jointLog] [info] Loading Quasi index
[2019-06-10 14:39:16.539] [jointLog] [info] Loading 32-bit quasi index
[2019-06-10 14:39:16.539] [stderrLog] [info] Loading Suffix Array 
[2019-06-10 14:39:17.841] [stderrLog] [info] Loading Transcript Info 
[2019-06-10 14:39:18.312] [stderrLog] [info] Loading Rank-Select Bit Array
[2019-06-10 14:39:18.415] [stderrLog] [info] There were 861,197 set bits in the bit array
[2019-06-10 14:39:18.485] [stderrLog] [info] Computing transcript lengths
[2019-06-10 14:39:18.486] [stderrLog] [info] Waiting to finish loading hash
[2019-06-10 14:39:33.238] [jointLog] [info] done
[2019-06-10 14:39:33.238] [jointLog] [info] Index contained 861,197 targets
[2019-06-10 14:39:33.238] [stderrLog] [info] Done loading index






processed 500,000 fragments
hits: 921,062, hits per frag:  2.08569

processed 1,000,000 fragments
hits: 1,845,859, hits per frag:  1.91604

processed 1,500,001 fragments
hits: 2,771,806, hits per frag:  1.90799

processed 2,000,002 fragments
hits: 3,697,228, hits per frag:  1.86861

processed 2,500,000 fragments
hits: 4,617,772, hits per frag:  1.95832

processed 3,000,001 fragments
hits: 5,541,406, hits per frag:  1.86928

processed 3,500,001 fragments
hits: 6,462,371, hits per frag:  1.92963

processed 4,000,000 fragments
hits: 7,383,039, hits per frag:  1.89124

processed 4,500,001 fragments
hits: 8,302,320, hits per frag:  1.85667

processed 5,000,000 fragments
hits: 9,226,844, hits per frag:  1.85875

processed 5,500,000 fragments
hits: 10,158,198, hits per frag:  1.87131

processed 6,000,000 fragments
hits: 11,086,805, hits per frag:  1.87076

processed 6,500,000 fragments
hits: 12,018,945, hits per frag:  1.85833

processed 6,500,032 fragments
hits: 12,018,992, hits per frag:  1.86236

processed 7,000,000 fragments
hits: 12,952,520, hits per frag:  1.86163

processed 7,500,000 fragments
hits: 13,883,627, hits per frag:  1.88966

processed 8,000,001 fragments
hits: 14,810,467, hits per frag:  1.86212

processed 8,500,001 fragments
hits: 15,735,626, hits per frag:  1.8774

processed 9,000,000 fragments
hits: 16,660,066, hits per frag:  1.86568

processed 9,500,000 fragments
hits: 17,580,131, hits per frag:  1.86431

processed 10,000,000 fragments
hits: 18,504,986, hits per frag:  1.86612

processed 10,500,001 fragments
hits: 19,429,486, hits per frag:  1.86285

processed 11,000,000 fragments
hits: 20,351,852, hits per frag:  1.87227

processed 11,500,000 fragments
hits: 21,276,005, hits per frag:  1.8541

processed 12,000,000 fragments
hits: 22,196,740, hits per frag:  1.86645

processed 12,500,000 fragments
hits: 23,112,458, hits per frag:  1.86559

processed 13,000,000 fragments
hits: 24,032,809, hits per frag:  1.85869

processed 13,500,000 fragments
hits: 24,950,782, hits per frag:  1.87358

processed 14,000,000 fragments
hits: 25,873,200, hits per frag:  1.85233

processed 14,500,000 fragments
hits: 26,806,589, hits per frag:  1.85031

processed 15,000,000 fragments
hits: 27,749,531, hits per frag:  1.85673

processed 15,500,000 fragments
hits: 28,696,294, hits per frag:  1.85796

processed 16,000,000 fragments
hits: 29,630,382, hits per frag:  1.85475

processed 16,500,000 fragments
hits: 30,559,714, hits per frag:  1.85453

processed 17,000,002 fragments
hits: 31,492,603, hits per frag:  1.86196

processed 17,500,000 fragments
hits: 32,420,498, hits per frag:  1.86786

processed 18,000,000 fragments
hits: 33,345,975, hits per frag:  1.85644[2019-06-10 14:40:21.733] [jointLog] [info] Thread saw mini-batch with a maximum of 17.52% zero probability fragments
[2019-06-10 14:40:21.733] [jointLog] [info] Thread saw mini-batch with a maximum of 17.80% zero probability fragments
[2019-06-10 14:40:21.733] [jointLog] [info] Thread saw mini-batch with a maximum of 17.76% zero probability fragments
[2019-06-10 14:40:21.733] [jointLog] [info] Thread saw mini-batch with a maximum of 17.46% zero probability fragments
[2019-06-10 14:40:21.733] [jointLog] [info] Thread saw mini-batch with a maximum of 17.24% zero probability fragments
[2019-06-10 14:40:21.733] [jointLog] [info] Thread saw mini-batch with a maximum of 17.60% zero probability fragments
[2019-06-10 14:40:21.733] [jointLog] [info] Thread saw mini-batch with a maximum of 17.02% zero probability fragments
[2019-06-10 14:40:21.733] [jointLog] [info] Thread saw mini-batch with a maximum of 17.38% zero probability fragments
[2019-06-10 14:40:21.733] [jointLog] [info] Thread saw mini-batch with a maximum of 17.36% zero probability fragments
[2019-06-10 14:40:21.733] [jointLog] [info] Thread saw mini-batch with a maximum of 17.34% zero probability fragments
[2019-06-10 14:40:21.733] [jointLog] [info] Thread saw mini-batch with a maximum of 17.32% zero probability fragments
[2019-06-10 14:40:21.733] [jointLog] [info] Thread saw mini-batch with a maximum of 17.96% zero probability fragments
[2019-06-10 14:40:21.738] [jointLog] [info] Thread saw mini-batch with a maximum of 17.34% zero probability fragments
[2019-06-10 14:40:21.754] [jointLog] [info] Thread saw mini-batch with a maximum of 16.94% zero probability fragments
[2019-06-10 14:40:21.778] [jointLog] [info] Thread saw mini-batch with a maximum of 17.54% zero probability fragments
[2019-06-10 14:40:21.789] [jointLog] [info] Thread saw mini-batch with a maximum of 17.44% zero probability fragments
[2019-06-10 14:40:21.792] [jointLog] [info] Thread saw mini-batch with a maximum of 17.58% zero probability fragments
[2019-06-10 14:40:21.795] [jointLog] [info] Thread saw mini-batch with a maximum of 17.58% zero probability fragments
[2019-06-10 14:40:21.814] [jointLog] [info] Thread saw mini-batch with a maximum of 17.70% zero probability fragments
[2019-06-10 14:40:21.818] [jointLog] [info] Thread saw mini-batch with a maximum of 17.68% zero probability fragments
[2019-06-10 14:40:21.831] [jointLog] [info] Thread saw mini-batch with a maximum of 17.68% zero probability fragments
[2019-06-10 14:40:21.837] [jointLog] [info] Thread saw mini-batch with a maximum of 17.88% zero probability fragments
[2019-06-10 14:40:21.849] [jointLog] [info] Thread saw mini-batch with a maximum of 17.52% zero probability fragments










[2019-06-10 14:40:22.233] [jointLog] [info] Computed 520,969 rich equivalence classes for further processing
[2019-06-10 14:40:22.233] [jointLog] [info] Counted 11,221,145 total reads in the equivalence classes 
[2019-06-10 14:40:22.258] [jointLog] [warning] 0.0114771% of fragments were shorter than the k used to build the index (31).
If this fraction is too large, consider re-building the index with a smaller k.
The minimum read size found was 20.


[2019-06-10 14:40:22.258] [jointLog] [info] Mapping rate = 61.0942%

[2019-06-10 14:40:22.258] [jointLog] [info] finished quantifyLibrary()
[2019-06-10 14:40:22.261] [jointLog] [info] Starting optimizer
[2019-06-10 14:40:22.655] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2019-06-10 14:40:22.680] [jointLog] [info] iteration = 0 | max rel diff. = 599.124
[2019-06-10 14:40:25.064] [jointLog] [info] iteration = 100 | max rel diff. = 20.341
[2019-06-10 14:40:27.417] [jointLog] [info] iteration = 200 | max rel diff. = 7.69976
[2019-06-10 14:40:29.773] [jointLog] [info] iteration = 300 | max rel diff. = 1.82553
[2019-06-10 14:40:31.984] [jointLog] [info] iteration = 400 | max rel diff. = 0.433124
[2019-06-10 14:40:34.342] [jointLog] [info] iteration = 500 | max rel diff. = 0.526591
[2019-06-10 14:40:36.752] [jointLog] [info] iteration = 600 | max rel diff. = 0.273749
[2019-06-10 14:40:39.169] [jointLog] [info] iteration = 700 | max rel diff. = 0.201873
[2019-06-10 14:40:41.523] [jointLog] [info] iteration = 800 | max rel diff. = 0.0619172
[2019-06-10 14:40:43.914] [jointLog] [info] iteration = 900 | max rel diff. = 0.0255884
[2019-06-10 14:40:46.218] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.0189579
[2019-06-10 14:40:48.687] [jointLog] [info] iteration = 1,100 | max rel diff. = 0.0503362
[2019-06-10 14:40:51.041] [jointLog] [info] iteration = 1,200 | max rel diff. = 0.274527
[2019-06-10 14:40:53.372] [jointLog] [info] iteration = 1,300 | max rel diff. = 0.0299212
[2019-06-10 14:40:54.243] [jointLog] [info] iteration = 1,339 | max rel diff. = 0.00675025
[2019-06-10 14:40:54.302] [jointLog] [info] Finished optimizer
[2019-06-10 14:40:54.302] [jointLog] [info] writing output 

CMD: /home/shared/Trinityrnaseq-v2.8.5/util/support_scripts/salmon_trans_to_gene_results.pl male_bleached_K5_02/quant.sf /media/sam/4TB_toshiba/porites/20180419_trinity/Trinity.fasta.gene_trans_map > male_bleached_K5_02/quant.sf.genes
CMD: salmon quant -i /media/sam/4TB_toshiba/porites/20180419_trinity/Trinity.fasta.salmon_quasi.idx -l ISR -1 /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P07-AGTCAA-READ1-Sequences.txt.gz_val_1.fq.gz -2 /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P07-AGTCAA-READ2-Sequences.txt.gz_val_2.fq.gz -o male_bleached_K5_03  -p 23
### salmon (mapping-based) v0.12.0
### [ program ] => salmon 
### [ command ] => quant 
### [ index ] => { /media/sam/4TB_toshiba/porites/20180419_trinity/Trinity.fasta.salmon_quasi.idx }
### [ libType ] => { ISR }
### [ mates1 ] => { /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P07-AGTCAA-READ1-Sequences.txt.gz_val_1.fq.gz }
### [ mates2 ] => { /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P07-AGTCAA-READ2-Sequences.txt.gz_val_2.fq.gz }
### [ output ] => { male_bleached_K5_03 }
### [ threads ] => { 23 }
Logs will be written to male_bleached_K5_03/logs
[2019-06-10 14:41:12.043] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2019-06-10 14:41:12.043] [jointLog] [warning] 

NOTE: It appears you are running salmon without the `--validateMappings` option.
Mapping validation can generally improve both the sensitivity and specificity of mapping,
with only a moderate increase in use of computational resources. 
Unless there is a specific reason to do this (e.g. testing on clean simulated data),
`--validateMappings` is generally recommended.

[2019-06-10 14:41:12.043] [jointLog] [info] parsing read library format
[2019-06-10 14:41:12.043] [jointLog] [info] There is 1 library.
[2019-06-10 14:41:12.102] [jointLog] [info] Loading Quasi index
[2019-06-10 14:41:12.102] [jointLog] [info] Loading 32-bit quasi index
[2019-06-10 14:41:12.103] [stderrLog] [info] Loading Suffix Array 
[2019-06-10 14:41:13.444] [stderrLog] [info] Loading Transcript Info 
[2019-06-10 14:41:13.872] [stderrLog] [info] Loading Rank-Select Bit Array
[2019-06-10 14:41:13.973] [stderrLog] [info] There were 861,197 set bits in the bit array
[2019-06-10 14:41:14.043] [stderrLog] [info] Computing transcript lengths
[2019-06-10 14:41:14.044] [stderrLog] [info] Waiting to finish loading hash
[2019-06-10 14:41:29.563] [stderrLog] [info] Done loading index
[2019-06-10 14:41:29.563] [jointLog] [info] done
[2019-06-10 14:41:29.563] [jointLog] [info] Index contained 861,197 targets






processed 500,000 fragments
hits: 973,925, hits per frag:  1.97352

processed 1,000,000 fragments
hits: 1,948,735, hits per frag:  2.00672

processed 1,500,000 fragments
hits: 2,927,427, hits per frag:  2.19775

processed 2,000,000 fragments
hits: 3,905,150, hits per frag:  2.02007

processed 2,500,000 fragments
hits: 4,882,869, hits per frag:  1.9952

processed 3,000,000 fragments
hits: 5,858,811, hits per frag:  2.01952

processed 3,500,000 fragments
hits: 6,831,757, hits per frag:  1.97891

processed 4,000,000 fragments
hits: 7,803,822, hits per frag:  2.02138

processed 4,500,000 fragments
hits: 8,777,680, hits per frag:  1.99291

processed 5,000,000 fragments
hits: 9,749,468, hits per frag:  1.98671

processed 5,500,001 fragments
hits: 10,722,310, hits per frag:  1.9584

processed 6,000,000 fragments
hits: 11,691,128, hits per frag:  1.95662

processed 6,500,000 fragments
hits: 12,662,260, hits per frag:  1.96993

processed 7,000,000 fragments
hits: 13,640,367, hits per frag:  1.97916

processed 7,500,000 fragments
hits: 14,618,395, hits per frag:  1.98611

processed 8,000,000 fragments
hits: 15,598,128, hits per frag:  2.02394

processed 8,500,001 fragments
hits: 16,580,280, hits per frag:  1.95814

processed 9,000,000 fragments
hits: 17,564,262, hits per frag:  1.9635

processed 9,500,001 fragments
hits: 18,550,487, hits per frag:  1.96144

processed 10,000,001 fragments
hits: 19,532,092, hits per frag:  1.98322

processed 10,500,000 fragments
hits: 20,514,284, hits per frag:  1.97953

processed 11,000,001 fragments
hits: 21,494,822, hits per frag:  1.97383

processed 11,500,000 fragments
hits: 22,473,629, hits per frag:  1.9626

processed 12,000,000 fragments
hits: 23,451,788, hits per frag:  1.96595

processed 12,500,000 fragments
hits: 24,430,694, hits per frag:  1.96907

processed 13,000,000 fragments
hits: 25,403,816, hits per frag:  1.96021

processed 13,500,000 fragments
hits: 26,375,882, hits per frag:  1.97411

processed 14,000,000 fragments
hits: 27,349,075, hits per frag:  1.96144

processed 14,500,001 fragments
hits: 28,324,080, hits per frag:  1.96158

processed 15,000,000 fragments
hits: 29,297,100, hits per frag:  1.99026

processed 15,500,000 fragments
hits: 30,273,386, hits per frag:  1.96683

processed 16,000,000 fragments
hits: 31,248,336, hits per frag:  1.96002

processed 16,500,000 fragments
hits: 32,217,021, hits per frag:  1.95935

processed 17,000,000 fragments
hits: 33,186,725, hits per frag:  1.97409

processed 17,500,000 fragments
hits: 34,157,471, hits per frag:  1.95764

processed 18,000,000 fragments
hits: 35,127,431, hits per frag:  1.96362

processed 18,500,000 fragments
hits: 36,097,742, hits per frag:  1.95559

processed 19,000,000 fragments
hits: 37,066,940, hits per frag:  1.95434

processed 19,500,000 fragments
hits: 38,033,515, hits per frag:  1.95631

processed 20,000,000 fragments
hits: 39,020,977, hits per frag:  1.95465

processed 20,500,000 fragments
hits: 40,003,861, hits per frag:  1.95727

processed 21,000,000 fragments
hits: 40,994,812, hits per frag:  1.95457

processed 21,500,000 fragments
hits: 41,996,380, hits per frag:  1.96082

processed 22,000,000 fragments
hits: 42,985,413, hits per frag:  1.95844

processed 22,500,000 fragments
hits: 43,971,232, hits per frag:  1.95874

processed 23,000,000 fragments
hits: 44,955,287, hits per frag:  1.95556

processed 23,500,001 fragments
hits: 45,934,499, hits per frag:  1.95976

processed 24,000,000 fragments
hits: 46,922,883, hits per frag:  1.96255

processed 24,500,000 fragments
hits: 47,904,484, hits per frag:  1.97693

processed 25,000,000 fragments
hits: 48,882,816, hits per frag:  1.95651

processed 25,500,000 fragments
hits: 49,857,880, hits per frag:  1.95742[2019-06-10 14:42:41.306] [jointLog] [info] Thread saw mini-batch with a maximum of 10.88% zero probability fragments
[2019-06-10 14:42:41.306] [jointLog] [info] Thread saw mini-batch with a maximum of 10.42% zero probability fragments
[2019-06-10 14:42:41.306] [jointLog] [info] Thread saw mini-batch with a maximum of 10.30% zero probability fragments
[2019-06-10 14:42:41.306] [jointLog] [info] Thread saw mini-batch with a maximum of 10.74% zero probability fragments
[2019-06-10 14:42:41.306] [jointLog] [info] Thread saw mini-batch with a maximum of 10.64% zero probability fragments
[2019-06-10 14:42:41.306] [jointLog] [info] Thread saw mini-batch with a maximum of 10.42% zero probability fragments
[2019-06-10 14:42:41.306] [jointLog] [info] Thread saw mini-batch with a maximum of 10.50% zero probability fragments
[2019-06-10 14:42:41.306] [jointLog] [info] Thread saw mini-batch with a maximum of 10.68% zero probability fragments
[2019-06-10 14:42:41.306] [jointLog] [info] Thread saw mini-batch with a maximum of 10.38% zero probability fragments
[2019-06-10 14:42:41.306] [jointLog] [info] Thread saw mini-batch with a maximum of 10.28% zero probability fragments
[2019-06-10 14:42:41.306] [jointLog] [info] Thread saw mini-batch with a maximum of 10.50% zero probability fragments
[2019-06-10 14:42:41.307] [jointLog] [info] Thread saw mini-batch with a maximum of 10.22% zero probability fragments
[2019-06-10 14:42:41.324] [jointLog] [info] Thread saw mini-batch with a maximum of 10.56% zero probability fragments
[2019-06-10 14:42:41.324] [jointLog] [info] Thread saw mini-batch with a maximum of 10.48% zero probability fragments
[2019-06-10 14:42:41.340] [jointLog] [info] Thread saw mini-batch with a maximum of 10.74% zero probability fragments
[2019-06-10 14:42:41.351] [jointLog] [info] Thread saw mini-batch with a maximum of 10.44% zero probability fragments
[2019-06-10 14:42:41.367] [jointLog] [info] Thread saw mini-batch with a maximum of 10.98% zero probability fragments
[2019-06-10 14:42:41.384] [jointLog] [info] Thread saw mini-batch with a maximum of 10.42% zero probability fragments
[2019-06-10 14:42:41.388] [jointLog] [info] Thread saw mini-batch with a maximum of 10.66% zero probability fragments
[2019-06-10 14:42:41.398] [jointLog] [info] Thread saw mini-batch with a maximum of 10.76% zero probability fragments
[2019-06-10 14:42:41.401] [jointLog] [info] Thread saw mini-batch with a maximum of 10.48% zero probability fragments
[2019-06-10 14:42:41.419] [jointLog] [info] Thread saw mini-batch with a maximum of 10.34% zero probability fragments
[2019-06-10 14:42:41.429] [jointLog] [info] Thread saw mini-batch with a maximum of 10.42% zero probability fragments










[2019-06-10 14:42:41.815] [jointLog] [info] Computed 449,423 rich equivalence classes for further processing
[2019-06-10 14:42:41.815] [jointLog] [info] Counted 18,262,331 total reads in the equivalence classes 
[2019-06-10 14:42:41.841] [jointLog] [warning] 0.0136297% of fragments were shorter than the k used to build the index (31).
If this fraction is too large, consider re-building the index with a smaller k.
The minimum read size found was 20.


[2019-06-10 14:42:41.841] [jointLog] [info] Mapping rate = 70.4929%

[2019-06-10 14:42:41.841] [jointLog] [info] finished quantifyLibrary()
[2019-06-10 14:42:41.844] [jointLog] [info] Starting optimizer
[2019-06-10 14:42:42.253] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2019-06-10 14:42:42.278] [jointLog] [info] iteration = 0 | max rel diff. = 924.477
[2019-06-10 14:42:44.565] [jointLog] [info] iteration = 100 | max rel diff. = 18.9527
[2019-06-10 14:42:46.835] [jointLog] [info] iteration = 200 | max rel diff. = 1.08631
[2019-06-10 14:42:49.157] [jointLog] [info] iteration = 300 | max rel diff. = 1.62037
[2019-06-10 14:42:51.474] [jointLog] [info] iteration = 400 | max rel diff. = 1.96811
[2019-06-10 14:42:53.807] [jointLog] [info] iteration = 500 | max rel diff. = 7.86584
[2019-06-10 14:42:56.115] [jointLog] [info] iteration = 600 | max rel diff. = 0.453288
[2019-06-10 14:42:58.420] [jointLog] [info] iteration = 700 | max rel diff. = 13.6535
[2019-06-10 14:43:00.713] [jointLog] [info] iteration = 800 | max rel diff. = 0.514014
[2019-06-10 14:43:03.016] [jointLog] [info] iteration = 900 | max rel diff. = 0.965494
[2019-06-10 14:43:05.258] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.391846
[2019-06-10 14:43:07.448] [jointLog] [info] iteration = 1,100 | max rel diff. = 0.163003
[2019-06-10 14:43:09.634] [jointLog] [info] iteration = 1,200 | max rel diff. = 0.0559962
[2019-06-10 14:43:11.822] [jointLog] [info] iteration = 1,300 | max rel diff. = 0.12304
[2019-06-10 14:43:14.029] [jointLog] [info] iteration = 1,400 | max rel diff. = 0.0937155
[2019-06-10 14:43:16.171] [jointLog] [info] iteration = 1,500 | max rel diff. = 0.107818
[2019-06-10 14:43:18.351] [jointLog] [info] iteration = 1,600 | max rel diff. = 0.0639336
[2019-06-10 14:43:20.614] [jointLog] [info] iteration = 1,700 | max rel diff. = 0.0115986
[2019-06-10 14:43:22.739] [jointLog] [info] iteration = 1,800 | max rel diff. = 0.171978
[2019-06-10 14:43:24.828] [jointLog] [info] iteration = 1,898 | max rel diff. = 0.00682558
[2019-06-10 14:43:24.885] [jointLog] [info] Finished optimizer
[2019-06-10 14:43:24.885] [jointLog] [info] writing output 

CMD: /home/shared/Trinityrnaseq-v2.8.5/util/support_scripts/salmon_trans_to_gene_results.pl male_bleached_K5_03/quant.sf /media/sam/4TB_toshiba/porites/20180419_trinity/Trinity.fasta.gene_trans_map > male_bleached_K5_03/quant.sf.genes
CMD: salmon quant -i /media/sam/4TB_toshiba/porites/20180419_trinity/Trinity.fasta.salmon_quasi.idx -l ISR -1 /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P08-CTTGTA-READ1-Sequences.txt.gz_val_1.fq.gz -2 /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P08-CTTGTA-READ2-Sequences.txt.gz_val_2.fq.gz -o female_bleached_K5_04  -p 23
### salmon (mapping-based) v0.12.0
### [ program ] => salmon 
### [ command ] => quant 
### [ index ] => { /media/sam/4TB_toshiba/porites/20180419_trinity/Trinity.fasta.salmon_quasi.idx }
### [ libType ] => { ISR }
### [ mates1 ] => { /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P08-CTTGTA-READ1-Sequences.txt.gz_val_1.fq.gz }
### [ mates2 ] => { /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P08-CTTGTA-READ2-Sequences.txt.gz_val_2.fq.gz }
### [ output ] => { female_bleached_K5_04 }
### [ threads ] => { 23 }
Logs will be written to female_bleached_K5_04/logs
[2019-06-10 14:43:42.503] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2019-06-10 14:43:42.503] [jointLog] [warning] 

NOTE: It appears you are running salmon without the `--validateMappings` option.
Mapping validation can generally improve both the sensitivity and specificity of mapping,
with only a moderate increase in use of computational resources. 
Unless there is a specific reason to do this (e.g. testing on clean simulated data),
`--validateMappings` is generally recommended.

[2019-06-10 14:43:42.503] [jointLog] [info] parsing read library format
[2019-06-10 14:43:42.503] [jointLog] [info] There is 1 library.
[2019-06-10 14:43:42.561] [jointLog] [info] Loading Quasi index
[2019-06-10 14:43:42.561] [jointLog] [info] Loading 32-bit quasi index
[2019-06-10 14:43:42.561] [stderrLog] [info] Loading Suffix Array 
[2019-06-10 14:43:43.889] [stderrLog] [info] Loading Transcript Info 
[2019-06-10 14:43:44.316] [stderrLog] [info] Loading Rank-Select Bit Array
[2019-06-10 14:43:44.421] [stderrLog] [info] There were 861,197 set bits in the bit array
[2019-06-10 14:43:44.491] [stderrLog] [info] Computing transcript lengths
[2019-06-10 14:43:44.492] [stderrLog] [info] Waiting to finish loading hash
[2019-06-10 14:43:59.148] [stderrLog] [info] Done loading index
[2019-06-10 14:43:59.148] [jointLog] [info] done
[2019-06-10 14:43:59.149] [jointLog] [info] Index contained 861,197 targets






processed 500,001 fragments
hits: 947,990, hits per frag:  2.30009

processed 1,000,001 fragments
hits: 1,894,074, hits per frag:  2.1664

processed 1,500,000 fragments
hits: 2,843,724, hits per frag:  1.97248

processed 2,000,000 fragments
hits: 3,791,469, hits per frag:  1.94716

processed 2,500,000 fragments
hits: 4,743,603, hits per frag:  1.92355

processed 3,000,000 fragments
hits: 5,692,619, hits per frag:  1.98054

processed 3,500,000 fragments
hits: 6,637,771, hits per frag:  1.93693

processed 4,000,001 fragments
hits: 7,583,921, hits per frag:  1.90005

processed 4,500,000 fragments
hits: 8,532,115, hits per frag:  1.96688

processed 5,000,001 fragments
hits: 9,478,714, hits per frag:  1.96424

processed 5,500,000 fragments
hits: 10,425,880, hits per frag:  1.92471

processed 6,000,000 fragments
hits: 11,366,923, hits per frag:  1.99618

processed 6,500,001 fragments
hits: 12,309,229, hits per frag:  1.92639

processed 7,000,000 fragments
hits: 13,249,096, hits per frag:  1.9111

processed 7,500,000 fragments
hits: 14,203,504, hits per frag:  1.91062

processed 8,000,000 fragments
hits: 15,156,112, hits per frag:  1.89985

processed 8,500,001 fragments
hits: 16,114,266, hits per frag:  1.90261

processed 9,000,000 fragments
hits: 17,066,184, hits per frag:  1.92689

processed 9,500,000 fragments
hits: 18,027,433, hits per frag:  1.94733

processed 10,000,000 fragments
hits: 18,989,177, hits per frag:  1.91808

processed 10,500,000 fragments
hits: 19,946,718, hits per frag:  1.92204

processed 11,000,000 fragments
hits: 20,908,446, hits per frag:  1.91583

processed 11,500,000 fragments
hits: 21,867,411, hits per frag:  1.91513

processed 11,500,019 fragments
hits: 21,867,440, hits per frag:  1.90607

processed 12,000,000 fragments
hits: 22,820,683, hits per frag:  1.91509

processed 12,500,000 fragments
hits: 23,771,628, hits per frag:  1.91208

processed 13,000,000 fragments
hits: 24,720,615, hits per frag:  1.90579

processed 13,500,000 fragments
hits: 25,672,076, hits per frag:  1.90986

processed 14,000,000 fragments
hits: 26,616,405, hits per frag:  1.90298

processed 14,500,000 fragments
hits: 27,559,316, hits per frag:  1.91673

processed 15,500,000 fragments
hits: 29,459,917, hits per frag:  1.9125

processed 16,000,000 fragments
hits: 30,405,155, hits per frag:  1.91413

processed 16,500,000 fragments
hits: 31,352,281, hits per frag:  1.90645

processed 17,000,001 fragments
hits: 32,303,492, hits per frag:  1.90587

processed 17,500,001 fragments
hits: 33,250,970, hits per frag:  1.90724

processed 18,000,000 fragments
hits: 34,194,818, hits per frag:  1.90398

processed 18,500,000 fragments
hits: 35,135,927, hits per frag:  1.90149

processed 19,000,000 fragments
hits: 36,077,783, hits per frag:  1.9112

processed 19,500,000 fragments
hits: 37,023,746, hits per frag:  1.9053

processed 20,000,001 fragments
hits: 37,970,562, hits per frag:  1.90879

processed 20,500,000 fragments
hits: 38,912,997, hits per frag:  1.92147

processed 21,000,000 fragments
hits: 39,854,199, hits per frag:  1.90564

processed 21,500,000 fragments
hits: 40,801,429, hits per frag:  1.9032

processed 22,000,000 fragments
hits: 41,763,661, hits per frag:  1.91972

processed 22,500,001 fragments
hits: 42,721,511, hits per frag:  1.90107

processed 23,000,001 fragments
hits: 43,689,410, hits per frag:  1.90389

processed 23,500,000 fragments
hits: 44,669,430, hits per frag:  1.90278

processed 24,000,000 fragments
hits: 45,637,654, hits per frag:  1.9105

processed 24,500,000 fragments
hits: 46,598,115, hits per frag:  1.91296

processed 25,000,000 fragments
hits: 47,556,061, hits per frag:  1.92698

processed 25,500,002 fragments
hits: 48,511,112, hits per frag:  1.91023

processed 26,000,000 fragments
hits: 49,469,024, hits per frag:  1.90828

processed 26,500,000 fragments
hits: 50,432,582, hits per frag:  1.90797

processed 27,000,000 fragments
hits: 51,385,751, hits per frag:  1.90534

processed 27,500,000 fragments
hits: 52,336,978, hits per frag:  1.90718

processed 28,000,000 fragments
hits: 53,285,747, hits per frag:  1.90515[2019-06-10 14:45:12.572] [jointLog] [info] Thread saw mini-batch with a maximum of 11.08% zero probability fragments
[2019-06-10 14:45:12.572] [jointLog] [info] Thread saw mini-batch with a maximum of 11.34% zero probability fragments
[2019-06-10 14:45:12.572] [jointLog] [info] Thread saw mini-batch with a maximum of 11.26% zero probability fragments
[2019-06-10 14:45:12.572] [jointLog] [info] Thread saw mini-batch with a maximum of 11.54% zero probability fragments
[2019-06-10 14:45:12.572] [jointLog] [info] Thread saw mini-batch with a maximum of 10.98% zero probability fragments
[2019-06-10 14:45:12.572] [jointLog] [info] Thread saw mini-batch with a maximum of 10.86% zero probability fragments
[2019-06-10 14:45:12.572] [jointLog] [info] Thread saw mini-batch with a maximum of 11.42% zero probability fragments
[2019-06-10 14:45:12.572] [jointLog] [info] Thread saw mini-batch with a maximum of 11.24% zero probability fragments
[2019-06-10 14:45:12.572] [jointLog] [info] Thread saw mini-batch with a maximum of 11.12% zero probability fragments
[2019-06-10 14:45:12.572] [jointLog] [info] Thread saw mini-batch with a maximum of 11.18% zero probability fragments
[2019-06-10 14:45:12.572] [jointLog] [info] Thread saw mini-batch with a maximum of 11.08% zero probability fragments
[2019-06-10 14:45:12.578] [jointLog] [info] Thread saw mini-batch with a maximum of 11.20% zero probability fragments
[2019-06-10 14:45:12.583] [jointLog] [info] Thread saw mini-batch with a maximum of 10.86% zero probability fragments
[2019-06-10 14:45:12.603] [jointLog] [info] Thread saw mini-batch with a maximum of 11.30% zero probability fragments
[2019-06-10 14:45:12.621] [jointLog] [info] Thread saw mini-batch with a maximum of 10.92% zero probability fragments
[2019-06-10 14:45:12.624] [jointLog] [info] Thread saw mini-batch with a maximum of 11.56% zero probability fragments
[2019-06-10 14:45:12.642] [jointLog] [info] Thread saw mini-batch with a maximum of 11.34% zero probability fragments
[2019-06-10 14:45:12.644] [jointLog] [info] Thread saw mini-batch with a maximum of 11.16% zero probability fragments
[2019-06-10 14:45:12.650] [jointLog] [info] Thread saw mini-batch with a maximum of 10.92% zero probability fragments
[2019-06-10 14:45:12.666] [jointLog] [info] Thread saw mini-batch with a maximum of 11.04% zero probability fragments
[2019-06-10 14:45:12.669] [jointLog] [info] Thread saw mini-batch with a maximum of 11.16% zero probability fragments
[2019-06-10 14:45:12.681] [jointLog] [info] Thread saw mini-batch with a maximum of 11.22% zero probability fragments
[2019-06-10 14:45:12.691] [jointLog] [info] Thread saw mini-batch with a maximum of 10.88% zero probability fragments




[2019-06-10 14:45:13.101] [jointLog] [info] Computed 425,276 rich equivalence classes for further processing
[2019-06-10 14:45:13.101] [jointLog] [info] Counted 19,570,136 total reads in the equivalence classes 






[2019-06-10 14:45:13.122] [jointLog] [warning] 0.0118102% of fragments were shorter than the k used to build the index (31).
If this fraction is too large, consider re-building the index with a smaller k.
The minimum read size found was 20.


[2019-06-10 14:45:13.122] [jointLog] [info] Mapping rate = 69.0962%

[2019-06-10 14:45:13.122] [jointLog] [info] finished quantifyLibrary()
[2019-06-10 14:45:13.122] [jointLog] [info] Starting optimizer
[2019-06-10 14:45:13.526] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2019-06-10 14:45:13.551] [jointLog] [info] iteration = 0 | max rel diff. = 927.219
[2019-06-10 14:45:15.722] [jointLog] [info] iteration = 100 | max rel diff. = 20.2634
[2019-06-10 14:45:17.825] [jointLog] [info] iteration = 200 | max rel diff. = 11.3487
[2019-06-10 14:45:19.941] [jointLog] [info] iteration = 300 | max rel diff. = 2.00646
[2019-06-10 14:45:22.064] [jointLog] [info] iteration = 400 | max rel diff. = 8.18326
[2019-06-10 14:45:24.193] [jointLog] [info] iteration = 500 | max rel diff. = 1.16856
[2019-06-10 14:45:26.257] [jointLog] [info] iteration = 600 | max rel diff. = 0.615374
[2019-06-10 14:45:28.355] [jointLog] [info] iteration = 700 | max rel diff. = 1.98914
[2019-06-10 14:45:30.433] [jointLog] [info] iteration = 800 | max rel diff. = 2.20467
[2019-06-10 14:45:32.530] [jointLog] [info] iteration = 900 | max rel diff. = 0.0523174
[2019-06-10 14:45:34.493] [jointLog] [info] iteration = 1,000 | max rel diff. = 2.03236
[2019-06-10 14:45:36.482] [jointLog] [info] iteration = 1,100 | max rel diff. = 3.60759
[2019-06-10 14:45:38.567] [jointLog] [info] iteration = 1,200 | max rel diff. = 0.0860444
[2019-06-10 14:45:40.621] [jointLog] [info] iteration = 1,300 | max rel diff. = 0.150284
[2019-06-10 14:45:42.653] [jointLog] [info] iteration = 1,400 | max rel diff. = 0.0605263
[2019-06-10 14:45:44.709] [jointLog] [info] iteration = 1,500 | max rel diff. = 14.1947
[2019-06-10 14:45:46.780] [jointLog] [info] iteration = 1,600 | max rel diff. = 0.0256011
[2019-06-10 14:45:48.267] [jointLog] [info] iteration = 1,673 | max rel diff. = 0.00773462
[2019-06-10 14:45:48.324] [jointLog] [info] Finished optimizer
[2019-06-10 14:45:48.324] [jointLog] [info] writing output 

CMD: /home/shared/Trinityrnaseq-v2.8.5/util/support_scripts/salmon_trans_to_gene_results.pl female_bleached_K5_04/quant.sf /media/sam/4TB_toshiba/porites/20180419_trinity/Trinity.fasta.gene_trans_map > female_bleached_K5_04/quant.sf.genes
CMD: salmon quant -i /media/sam/4TB_toshiba/porites/20180419_trinity/Trinity.fasta.salmon_quasi.idx -l ISR -1 /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P09-GTGAAA-READ1-Sequences.txt.gz_val_1.fq.gz -2 /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P09-GTGAAA-READ2-Sequences.txt.gz_val_2.fq.gz -o female_bleached_K5_05  -p 23
### salmon (mapping-based) v0.12.0
### [ program ] => salmon 
### [ command ] => quant 
### [ index ] => { /media/sam/4TB_toshiba/porites/20180419_trinity/Trinity.fasta.salmon_quasi.idx }
### [ libType ] => { ISR }
### [ mates1 ] => { /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P09-GTGAAA-READ1-Sequences.txt.gz_val_1.fq.gz }
### [ mates2 ] => { /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P09-GTGAAA-READ2-Sequences.txt.gz_val_2.fq.gz }
### [ output ] => { female_bleached_K5_05 }
### [ threads ] => { 23 }
Logs will be written to female_bleached_K5_05/logs
[2019-06-10 14:46:06.545] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2019-06-10 14:46:06.545] [jointLog] [warning] 

NOTE: It appears you are running salmon without the `--validateMappings` option.
Mapping validation can generally improve both the sensitivity and specificity of mapping,
with only a moderate increase in use of computational resources. 
Unless there is a specific reason to do this (e.g. testing on clean simulated data),
`--validateMappings` is generally recommended.

[2019-06-10 14:46:06.545] [jointLog] [info] parsing read library format
[2019-06-10 14:46:06.545] [jointLog] [info] There is 1 library.
[2019-06-10 14:46:06.605] [jointLog] [info] Loading Quasi index
[2019-06-10 14:46:06.605] [jointLog] [info] Loading 32-bit quasi index
[2019-06-10 14:46:06.605] [stderrLog] [info] Loading Suffix Array 
[2019-06-10 14:46:07.924] [stderrLog] [info] Loading Transcript Info 
[2019-06-10 14:46:08.361] [stderrLog] [info] Loading Rank-Select Bit Array
[2019-06-10 14:46:08.466] [stderrLog] [info] There were 861,197 set bits in the bit array
[2019-06-10 14:46:08.536] [stderrLog] [info] Computing transcript lengths
[2019-06-10 14:46:08.537] [stderrLog] [info] Waiting to finish loading hash
[2019-06-10 14:46:23.919] [stderrLog] [info] Done loading index
[2019-06-10 14:46:23.919] [jointLog] [info] done
[2019-06-10 14:46:23.919] [jointLog] [info] Index contained 861,197 targets






processed 500,000 fragments
hits: 961,051, hits per frag:  1.98082

processed 1,000,000 fragments
hits: 1,923,122, hits per frag:  2.08841

processed 1,500,000 fragments
hits: 2,883,932, hits per frag:  2.01363

processed 2,000,001 fragments
hits: 3,843,124, hits per frag:  2.09114

processed 2,500,000 fragments
hits: 4,804,241, hits per frag:  2.1042

processed 3,000,000 fragments
hits: 5,763,150, hits per frag:  1.98187

processed 3,500,000 fragments
hits: 6,721,234, hits per frag:  2.01842

processed 4,000,000 fragments
hits: 7,676,682, hits per frag:  1.95137

processed 4,500,000 fragments
hits: 8,634,150, hits per frag:  1.95189

processed 5,000,000 fragments
hits: 9,589,648, hits per frag:  1.96076

processed 5,500,000 fragments
hits: 10,543,293, hits per frag:  1.93244

processed 6,000,000 fragments
hits: 11,504,712, hits per frag:  1.94372

processed 6,500,000 fragments
hits: 12,473,211, hits per frag:  1.93586

processed 7,000,000 fragments
hits: 13,438,724, hits per frag:  1.92825

processed 7,500,001 fragments
hits: 14,403,216, hits per frag:  1.93228

processed 8,000,000 fragments
hits: 15,370,517, hits per frag:  1.95851

processed 8,500,000 fragments
hits: 16,339,510, hits per frag:  1.94199

processed 9,000,000 fragments
hits: 17,301,753, hits per frag:  1.92872

processed 9,500,000 fragments
hits: 18,260,956, hits per frag:  1.95952

processed 10,000,002 fragments
hits: 19,221,551, hits per frag:  1.93802

processed 10,500,001 fragments
hits: 20,181,779, hits per frag:  1.96368

processed 11,000,000 fragments
hits: 21,135,953, hits per frag:  1.9382

processed 11,500,000 fragments
hits: 22,094,028, hits per frag:  1.95331

processed 12,000,000 fragments
hits: 23,053,821, hits per frag:  1.93689

processed 12,500,000 fragments
hits: 24,009,427, hits per frag:  1.94241

processed 13,000,000 fragments
hits: 24,964,828, hits per frag:  1.93154

processed 13,500,000 fragments
hits: 25,922,285, hits per frag:  1.9266

processed 14,000,000 fragments
hits: 26,875,380, hits per frag:  1.9383

processed 14,500,000 fragments
hits: 27,824,908, hits per frag:  1.94858

processed 15,000,000 fragments
hits: 28,775,908, hits per frag:  1.92462

processed 15,500,000 fragments
hits: 29,727,641, hits per frag:  1.92698

processed 16,000,000 fragments
hits: 30,678,788, hits per frag:  1.93561

processed 16,500,000 fragments
hits: 31,634,194, hits per frag:  1.91957

processed 17,000,000 fragments
hits: 32,604,335, hits per frag:  1.93395

processed 17,500,000 fragments
hits: 33,573,520, hits per frag:  1.92935

processed 18,000,000 fragments
hits: 34,547,514, hits per frag:  1.925

processed 18,500,000 fragments
hits: 35,523,543, hits per frag:  1.92262

processed 19,000,000 fragments
hits: 36,491,140, hits per frag:  1.94278

processed 19,500,000 fragments
hits: 37,455,566, hits per frag:  1.9297

processed 20,000,000 fragments
hits: 38,416,823, hits per frag:  1.92294

processed 20,500,000 fragments
hits: 39,382,987, hits per frag:  1.92388

processed 21,000,000 fragments
hits: 40,342,723, hits per frag:  1.92252

processed 21,500,000 fragments
hits: 41,301,041, hits per frag:  1.92857[2019-06-10 14:47:22.512] [jointLog] [info] Thread saw mini-batch with a maximum of 11.92% zero probability fragments
[2019-06-10 14:47:22.512] [jointLog] [info] Thread saw mini-batch with a maximum of 11.94% zero probability fragments
[2019-06-10 14:47:22.513] [jointLog] [info] Thread saw mini-batch with a maximum of 12.00% zero probability fragments
[2019-06-10 14:47:22.513] [jointLog] [info] Thread saw mini-batch with a maximum of 12.06% zero probability fragments
[2019-06-10 14:47:22.513] [jointLog] [info] Thread saw mini-batch with a maximum of 11.70% zero probability fragments
[2019-06-10 14:47:22.513] [jointLog] [info] Thread saw mini-batch with a maximum of 11.90% zero probability fragments
[2019-06-10 14:47:22.513] [jointLog] [info] Thread saw mini-batch with a maximum of 12.38% zero probability fragments
[2019-06-10 14:47:22.513] [jointLog] [info] Thread saw mini-batch with a maximum of 11.96% zero probability fragments
[2019-06-10 14:47:22.513] [jointLog] [info] Thread saw mini-batch with a maximum of 12.10% zero probability fragments
[2019-06-10 14:47:22.513] [jointLog] [info] Thread saw mini-batch with a maximum of 12.28% zero probability fragments
[2019-06-10 14:47:22.513] [jointLog] [info] Thread saw mini-batch with a maximum of 11.92% zero probability fragments
[2019-06-10 14:47:22.516] [jointLog] [info] Thread saw mini-batch with a maximum of 11.92% zero probability fragments
[2019-06-10 14:47:22.516] [jointLog] [info] Thread saw mini-batch with a maximum of 11.88% zero probability fragments
[2019-06-10 14:47:22.517] [jointLog] [info] Thread saw mini-batch with a maximum of 11.86% zero probability fragments
[2019-06-10 14:47:22.541] [jointLog] [info] Thread saw mini-batch with a maximum of 12.28% zero probability fragments
[2019-06-10 14:47:22.549] [jointLog] [info] Thread saw mini-batch with a maximum of 12.04% zero probability fragments
[2019-06-10 14:47:22.567] [jointLog] [info] Thread saw mini-batch with a maximum of 11.70% zero probability fragments
[2019-06-10 14:47:22.579] [jointLog] [info] Thread saw mini-batch with a maximum of 11.98% zero probability fragments
[2019-06-10 14:47:22.592] [jointLog] [info] Thread saw mini-batch with a maximum of 12.20% zero probability fragments
[2019-06-10 14:47:22.592] [jointLog] [info] Thread saw mini-batch with a maximum of 11.84% zero probability fragments
[2019-06-10 14:47:22.594] [jointLog] [info] Thread saw mini-batch with a maximum of 12.20% zero probability fragments
[2019-06-10 14:47:22.610] [jointLog] [info] Thread saw mini-batch with a maximum of 11.90% zero probability fragments
[2019-06-10 14:47:22.638] [jointLog] [info] Thread saw mini-batch with a maximum of 12.10% zero probability fragments










[2019-06-10 14:47:23.068] [jointLog] [info] Computed 379,201 rich equivalence classes for further processing
[2019-06-10 14:47:23.068] [jointLog] [info] Counted 14,941,052 total reads in the equivalence classes 
[2019-06-10 14:47:23.095] [jointLog] [warning] 0.0194906% of fragments were shorter than the k used to build the index (31).
If this fraction is too large, consider re-building the index with a smaller k.
The minimum read size found was 20.


[2019-06-10 14:47:23.095] [jointLog] [info] Mapping rate = 68.2791%

[2019-06-10 14:47:23.098] [jointLog] [info] finished quantifyLibrary()
[2019-06-10 14:47:23.098] [jointLog] [info] Starting optimizer
[2019-06-10 14:47:23.436] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2019-06-10 14:47:23.464] [jointLog] [info] iteration = 0 | max rel diff. = 705.907
[2019-06-10 14:47:25.569] [jointLog] [info] iteration = 100 | max rel diff. = 10.9157
[2019-06-10 14:47:27.649] [jointLog] [info] iteration = 200 | max rel diff. = 6.32877
[2019-06-10 14:47:29.806] [jointLog] [info] iteration = 300 | max rel diff. = 7.90823
[2019-06-10 14:47:31.884] [jointLog] [info] iteration = 400 | max rel diff. = 0.735216
[2019-06-10 14:47:33.918] [jointLog] [info] iteration = 500 | max rel diff. = 0.841352
[2019-06-10 14:47:35.900] [jointLog] [info] iteration = 600 | max rel diff. = 0.490164
[2019-06-10 14:47:37.865] [jointLog] [info] iteration = 700 | max rel diff. = 1.33158
[2019-06-10 14:47:39.826] [jointLog] [info] iteration = 800 | max rel diff. = 0.293466
[2019-06-10 14:47:41.764] [jointLog] [info] iteration = 900 | max rel diff. = 0.262171
[2019-06-10 14:47:43.763] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.0443271
[2019-06-10 14:47:45.792] [jointLog] [info] iteration = 1,100 | max rel diff. = 0.343566
[2019-06-10 14:47:47.707] [jointLog] [info] iteration = 1,200 | max rel diff. = 0.0716914
[2019-06-10 14:47:49.671] [jointLog] [info] iteration = 1,300 | max rel diff. = 3.41002
[2019-06-10 14:47:51.574] [jointLog] [info] iteration = 1,400 | max rel diff. = 0.0152851
[2019-06-10 14:47:53.507] [jointLog] [info] iteration = 1,500 | max rel diff. = 0.0313933
[2019-06-10 14:47:55.448] [jointLog] [info] iteration = 1,600 | max rel diff. = 0.397269
[2019-06-10 14:47:55.526] [jointLog] [info] iteration = 1,605 | max rel diff. = 0.00252452
[2019-06-10 14:47:55.581] [jointLog] [info] Finished optimizer
[2019-06-10 14:47:55.581] [jointLog] [info] writing output 

CMD: /home/shared/Trinityrnaseq-v2.8.5/util/support_scripts/salmon_trans_to_gene_results.pl female_bleached_K5_05/quant.sf /media/sam/4TB_toshiba/porites/20180419_trinity/Trinity.fasta.gene_trans_map > female_bleached_K5_05/quant.sf.genes
CMD: salmon quant -i /media/sam/4TB_toshiba/porites/20180419_trinity/Trinity.fasta.salmon_quasi.idx -l ISR -1 /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P13-ATCACG-READ1-Sequences.txt.gz_val_1.fq.gz -2 /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P13-ATCACG-READ2-Sequences.txt.gz_val_2.fq.gz -o female_bleached_K5_06  -p 23
### salmon (mapping-based) v0.12.0
### [ program ] => salmon 
### [ command ] => quant 
### [ index ] => { /media/sam/4TB_toshiba/porites/20180419_trinity/Trinity.fasta.salmon_quasi.idx }
### [ libType ] => { ISR }
### [ mates1 ] => { /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P13-ATCACG-READ1-Sequences.txt.gz_val_1.fq.gz }
### [ mates2 ] => { /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P13-ATCACG-READ2-Sequences.txt.gz_val_2.fq.gz }
### [ output ] => { female_bleached_K5_06 }
### [ threads ] => { 23 }
Logs will be written to female_bleached_K5_06/logs
[2019-06-10 14:48:13.415] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2019-06-10 14:48:13.415] [jointLog] [warning] 

NOTE: It appears you are running salmon without the `--validateMappings` option.
Mapping validation can generally improve both the sensitivity and specificity of mapping,
with only a moderate increase in use of computational resources. 
Unless there is a specific reason to do this (e.g. testing on clean simulated data),
`--validateMappings` is generally recommended.

[2019-06-10 14:48:13.415] [jointLog] [info] parsing read library format
[2019-06-10 14:48:13.415] [jointLog] [info] There is 1 library.
[2019-06-10 14:48:13.474] [jointLog] [info] Loading Quasi index
[2019-06-10 14:48:13.474] [jointLog] [info] Loading 32-bit quasi index
[2019-06-10 14:48:13.474] [stderrLog] [info] Loading Suffix Array 
[2019-06-10 14:48:14.811] [stderrLog] [info] Loading Transcript Info 
[2019-06-10 14:48:15.237] [stderrLog] [info] Loading Rank-Select Bit Array
[2019-06-10 14:48:15.339] [stderrLog] [info] There were 861,197 set bits in the bit array
[2019-06-10 14:48:15.409] [stderrLog] [info] Computing transcript lengths
[2019-06-10 14:48:15.410] [stderrLog] [info] Waiting to finish loading hash
[2019-06-10 14:48:30.968] [stderrLog] [info] Done loading index
[2019-06-10 14:48:30.968] [jointLog] [info] done
[2019-06-10 14:48:30.968] [jointLog] [info] Index contained 861,197 targets






processed 500,000 fragments
hits: 829,395, hits per frag:  1.79719

processed 1,000,001 fragments
hits: 1,662,441, hits per frag:  1.76681

processed 1,500,000 fragments
hits: 2,493,355, hits per frag:  1.71819

processed 2,000,000 fragments
hits: 3,323,015, hits per frag:  1.70313

processed 2,500,000 fragments
hits: 4,152,112, hits per frag:  1.68802

processed 3,000,000 fragments
hits: 4,979,883, hits per frag:  1.74367

processed 3,500,001 fragments
hits: 5,808,885, hits per frag:  1.71081

processed 4,000,001 fragments
hits: 6,633,078, hits per frag:  1.67646

processed 4,500,000 fragments
hits: 7,463,097, hits per frag:  1.72322

processed 5,000,000 fragments
hits: 8,299,047, hits per frag:  1.67358

processed 5,500,000 fragments
hits: 9,140,373, hits per frag:  1.74592

processed 6,000,000 fragments
hits: 9,981,655, hits per frag:  1.68794

processed 6,500,001 fragments
hits: 10,819,455, hits per frag:  1.69751

processed 7,000,001 fragments
hits: 11,654,351, hits per frag:  1.72607

processed 7,500,000 fragments
hits: 12,485,994, hits per frag:  1.69021

processed 8,000,000 fragments
hits: 13,321,401, hits per frag:  1.69813

processed 8,500,000 fragments
hits: 14,149,926, hits per frag:  1.66638

processed 9,000,000 fragments
hits: 14,976,800, hits per frag:  1.68119

processed 9,500,000 fragments
hits: 15,806,677, hits per frag:  1.67392

processed 10,000,000 fragments
hits: 16,633,324, hits per frag:  1.67099

processed 10,500,000 fragments
hits: 17,462,259, hits per frag:  1.67667

processed 11,000,001 fragments
hits: 18,287,486, hits per frag:  1.68249

processed 11,500,000 fragments
hits: 19,110,973, hits per frag:  1.67168

processed 12,000,000 fragments
hits: 19,935,801, hits per frag:  1.67991

processed 12,500,000 fragments
hits: 20,761,392, hits per frag:  1.68426

processed 13,000,001 fragments
hits: 21,584,991, hits per frag:  1.67055

processed 13,500,000 fragments
hits: 22,424,319, hits per frag:  1.67308

processed 14,000,000 fragments
hits: 23,263,770, hits per frag:  1.70308

processed 14,500,001 fragments
hits: 24,113,544, hits per frag:  1.66614

processed 15,000,001 fragments
hits: 24,955,607, hits per frag:  1.67152

processed 15,500,000 fragments
hits: 25,794,762, hits per frag:  1.68689

processed 16,000,000 fragments
hits: 26,632,684, hits per frag:  1.67372

processed 16,500,000 fragments
hits: 27,467,116, hits per frag:  1.66865

processed 17,000,000 fragments
hits: 28,297,393, hits per frag:  1.66881[2019-06-10 14:49:17.595] [jointLog] [info] Thread saw mini-batch with a maximum of 11.40% zero probability fragments
[2019-06-10 14:49:17.595] [jointLog] [info] Thread saw mini-batch with a maximum of 10.76% zero probability fragments
[2019-06-10 14:49:17.595] [jointLog] [info] Thread saw mini-batch with a maximum of 10.98% zero probability fragments
[2019-06-10 14:49:17.595] [jointLog] [info] Thread saw mini-batch with a maximum of 10.88% zero probability fragments
[2019-06-10 14:49:17.595] [jointLog] [info] Thread saw mini-batch with a maximum of 10.56% zero probability fragments
[2019-06-10 14:49:17.595] [jointLog] [info] Thread saw mini-batch with a maximum of 10.76% zero probability fragments
[2019-06-10 14:49:17.595] [jointLog] [info] Thread saw mini-batch with a maximum of 10.58% zero probability fragments
[2019-06-10 14:49:17.595] [jointLog] [info] Thread saw mini-batch with a maximum of 11.08% zero probability fragments
[2019-06-10 14:49:17.595] [jointLog] [info] Thread saw mini-batch with a maximum of 11.32% zero probability fragments
[2019-06-10 14:49:17.595] [jointLog] [info] Thread saw mini-batch with a maximum of 10.54% zero probability fragments
[2019-06-10 14:49:17.595] [jointLog] [info] Thread saw mini-batch with a maximum of 10.66% zero probability fragments
[2019-06-10 14:49:17.595] [jointLog] [info] Thread saw mini-batch with a maximum of 10.74% zero probability fragments
[2019-06-10 14:49:17.595] [jointLog] [info] Thread saw mini-batch with a maximum of 10.56% zero probability fragments
[2019-06-10 14:49:17.606] [jointLog] [info] Thread saw mini-batch with a maximum of 10.62% zero probability fragments
[2019-06-10 14:49:17.610] [jointLog] [info] Thread saw mini-batch with a maximum of 10.80% zero probability fragments
[2019-06-10 14:49:17.615] [jointLog] [info] Thread saw mini-batch with a maximum of 10.82% zero probability fragments
[2019-06-10 14:49:17.635] [jointLog] [info] Thread saw mini-batch with a maximum of 10.66% zero probability fragments
[2019-06-10 14:49:17.639] [jointLog] [info] Thread saw mini-batch with a maximum of 10.76% zero probability fragments
[2019-06-10 14:49:17.655] [jointLog] [info] Thread saw mini-batch with a maximum of 10.94% zero probability fragments
[2019-06-10 14:49:17.666] [jointLog] [info] Thread saw mini-batch with a maximum of 10.72% zero probability fragments
[2019-06-10 14:49:17.678] [jointLog] [info] Thread saw mini-batch with a maximum of 10.72% zero probability fragments
[2019-06-10 14:49:17.681] [jointLog] [info] Thread saw mini-batch with a maximum of 10.66% zero probability fragments
[2019-06-10 14:49:17.703] [jointLog] [info] Thread saw mini-batch with a maximum of 11.08% zero probability fragments










[2019-06-10 14:49:18.106] [jointLog] [info] Computed 325,824 rich equivalence classes for further processing
[2019-06-10 14:49:18.106] [jointLog] [info] Counted 11,685,920 total reads in the equivalence classes 
[2019-06-10 14:49:18.129] [jointLog] [warning] 0.0100547% of fragments were shorter than the k used to build the index (31).
If this fraction is too large, consider re-building the index with a smaller k.
The minimum read size found was 20.


[2019-06-10 14:49:18.129] [jointLog] [info] Mapping rate = 67.6054%

[2019-06-10 14:49:18.129] [jointLog] [info] finished quantifyLibrary()
[2019-06-10 14:49:18.129] [jointLog] [info] Starting optimizer
[2019-06-10 14:49:18.534] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2019-06-10 14:49:18.558] [jointLog] [info] iteration = 0 | max rel diff. = 705.518
[2019-06-10 14:49:20.679] [jointLog] [info] iteration = 100 | max rel diff. = 17.0384
[2019-06-10 14:49:22.688] [jointLog] [info] iteration = 200 | max rel diff. = 5.61053
[2019-06-10 14:49:24.716] [jointLog] [info] iteration = 300 | max rel diff. = 2.86227
[2019-06-10 14:49:26.778] [jointLog] [info] iteration = 400 | max rel diff. = 0.757619
[2019-06-10 14:49:28.728] [jointLog] [info] iteration = 500 | max rel diff. = 1.61255
[2019-06-10 14:49:30.778] [jointLog] [info] iteration = 600 | max rel diff. = 7.47305
[2019-06-10 14:49:32.742] [jointLog] [info] iteration = 700 | max rel diff. = 0.102248
[2019-06-10 14:49:34.792] [jointLog] [info] iteration = 800 | max rel diff. = 0.207691
[2019-06-10 14:49:36.825] [jointLog] [info] iteration = 900 | max rel diff. = 0.254125
[2019-06-10 14:49:38.752] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.23089
[2019-06-10 14:49:40.734] [jointLog] [info] iteration = 1,100 | max rel diff. = 0.0913661
[2019-06-10 14:49:42.691] [jointLog] [info] iteration = 1,200 | max rel diff. = 0.231964
[2019-06-10 14:49:44.718] [jointLog] [info] iteration = 1,300 | max rel diff. = 1.2626
[2019-06-10 14:49:46.621] [jointLog] [info] iteration = 1,400 | max rel diff. = 0.099466
[2019-06-10 14:49:46.826] [jointLog] [info] iteration = 1,412 | max rel diff. = 0.00200641
[2019-06-10 14:49:46.875] [jointLog] [info] Finished optimizer
[2019-06-10 14:49:46.875] [jointLog] [info] writing output 

CMD: /home/shared/Trinityrnaseq-v2.8.5/util/support_scripts/salmon_trans_to_gene_results.pl female_bleached_K5_06/quant.sf /media/sam/4TB_toshiba/porites/20180419_trinity/Trinity.fasta.gene_trans_map > female_bleached_K5_06/quant.sf.genes